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Yes, pre workflow hooks defined in your server config file are always respected and executed before any workflow runs, including custom workflows defined in the repo-level atlantis.yaml. The execution of these hooks is independent of whether you use the default workflow or a custom one—there’s no code path that disables or overrides server-level pre workflow hooks when a custom workflow is present. If a pre workflow hook fails and you have the fail-on-pre-workflow-hook-error flag set, the main workflow (custom or default) will not run; otherwise, Atlantis will proceed with the workflow even if the pre hook fails. You can see this logic in the pre workflow hooks runner implementation and …

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@paymog
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